Article
Fisheries
Dan Qiao, Yanjing Zhao, Chao Pei, Xianliang Zhao, Xinyu Jiang, Lei Zhu, Jie Zhang, Li Li, Xianghui Kong
Summary: This study identified and characterized 61 CC chemokines from allotetraploid common carp, revealing their unique features in cell migration, gene arrangement, and chromosomal location. Additionally, the study predicted and verified the antimicrobial activity of certain CC chemokines, highlighting their important role in immune system evolution and pathogen infection.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca, Samuele Greco, Marco Gerdol, Maria Assunta Biscotti
Summary: This study found a link between TEs in fish genomes and species with migratory behavior, but did not confirm higher relative abundance of DNA transposons in ray-finned fish. There were no clear differences in the relative contribution of different TE types in migratory ray-finned species, but a significant relationship between migratory behavior and differences in SINEs quantity was reported.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Zijiang Yang, Shanshan Chen, Shufen Wang, Ying Hu, Guanghui Zhang, Yang Dong, Shengchao Yang, Jianhua Miao, Wei Chen, Jun Sheng
Summary: A high-quality genome assembly of Siberian ginseng was reported, revealing a high proportion of transposable elements and a large number of predicted protein-coding genes. Comparative analysis with other plant genomes showed that whole-genome duplication events and a burst expansion of chromoviral elements may have contributed to adaptation in the Araliaceae family.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Yongbo Liu, Yi Zhou, Feng Cheng, Renchao Zhou, Yinqing Yang, Yanchang Wang, Xingtan Zhang, Douglas E. Soltis, Nengwen Xiao, Zhanjun Quan, Junsheng Li
Summary: This research provides evidence that much of the hexaploid genome of Actinidia deliciosa matches the diploid Actinidia chinensis. However, comparisons of intra- and intergenome synteny indicate chromosomal changes. The highly diversified pattern of gene expression and rapid population expansion after polyploidization likely facilitated the adaptation and niche differentiation of A. deliciosa in nature.
Article
Plant Sciences
Lingfei Li, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos-Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C. Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong-Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong Li, Sunil Kumar Sahu, Huanming Yang, Ernest Wu, Joel Sharbrough, Michael Lisby, Xin Liu, Xun Xu, Douglas E. Soltis, Yves Van de Peer, Catherine Kidner, Shouzhou Zhang, Huan Liu
Summary: This study investigates the lineage evolution and shade adaptation of Begonia, one of the most species-rich angiosperm genera, using chromosome-scale genome assemblies for four species and additional genomic data. The results reveal a lineage-specific whole-genome duplication event and expansions of gene families related to shade adaptation.
Article
Biochemistry & Molecular Biology
Manu Kumar Gundappa, Thu-Hien To, Lars Gronvold, Samuel A. M. Martin, Sigbjorn Lien, Juergen Geist, David Hazlerigg, Simen R. Sandve, Daniel J. Macqueen
Summary: This study investigates the long-term outcomes of autopolyploid rediploidization in salmonid fishes using genome-wide resolution. Analysis reveals an initial wave of rediploidization in the late Cretaceous followed by a period of genomic stasis and a second rediploidization wave in the early Eocene, coinciding with species diversification. Insights into potential functional outcomes of delayed rediploidization are provided through gene set enrichment, gene expression, and codon-based selection analyses. The study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
Xi Zhang, David Roy Smith
Summary: This article provides a summary of research tools used for detecting gene duplicates, including metrics, computational approaches, and the latest developments in web tools and databases.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Akihiro Ezoe, Kazumasa Shirai, Kousuke Hanada
Summary: Gene duplication is a major mechanism for creating new genes in plants, resulting in duplicated genes with varying degrees of functional diversification. High diversified duplicates from tandem duplications tend to have lineage-specific functions, while low diversified duplicates from whole-genome duplications are related to essential signaling pathways, impacting plant evolution differently.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Jun He, Zhongyu Yu, Jiafu Jiang, Sumei Chen, Weimin Fang, Zhiyong Guan, Yuan Liao, Zhenxing Wang, Fadi Chen, Haibin Wang
Summary: Whole genome duplication, especially autopolyploidization, leads to genetic changes such as loss of old fragments and gain of novel fragments, including potential LTR retrotransposons. Ty1-copia and Ty3-gypsy elements were evaluated using molecular marker techniques, suggesting that autopolyploidization may accelerate the evolutionary process among progenies through perturbations of LTR retrotransposons. The need to expand the current evolutionary framework to include a genetic dimension when studying genomic shock following autopolyploidization in Asteraceae is strongly recommended.
Article
Biotechnology & Applied Microbiology
Sophie Fouchecourt, Valerie Fillon, Christelle Marrauld, Caroline Callot, Sarah Ronsin, Floriane Picolo, Cecile Douet, Benoit Piegu, Philippe Monget
Summary: Gene duplications increase genetic and phenotypic diversity. PHF7 gene is a highly duplicated gene family in the chicken genome, which is also likely to occur in other bird species. By screening the chicken BAC library and using FISH technology, we identified and located 10 PHF7-like loci on five Gallus gallus chromosomes. The sequenced BAC sequences revealed additional duplicated genes in these genomic regions.
Article
Plant Sciences
Ruoqiu Wang, Bin Wu, Jianbo Jian, Yiwei Tang, Ticao Zhang, Zhiping Song, Wenju Zhang, La Qiong
Summary: This study assembled the genome of Hippophae tibetana using PacBio Hifi platform and Hi-C technology, and inferred its sexual chromosome. Two whole-genome duplication events and retroelements amplifications were detected. Comparing with related species at lower altitude, H. tibetana had rapid evolving genes involved in adaptation to high altitude habitats. However, comparing with Hippophae rhamnoides, no rapid evolving genes were found except microtubule and microtubule-based process genes. H. tibetana has a larger genome with more transposable elements and genes, increasing genome variability and expression plasticity.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Luis Diaz-Garcia, Luis Fernando Garcia-Ortega, Maria Gonzalez-Rodriguez, Luis Delaye, Massimo Iorizzo, Juan Zalapa
Summary: The American cranberry is an important fruit crop model due to its unique fruit composition, recent domestication, and various reproductive modes. This study presents the first chromosome-scale genome assembly of cranberry, providing insights into its genetic history and evolutionary relationships with other plant species. Phylogenetic analysis also identified potential regulators of anthocyanin biosynthesis in cranberry fruit.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Gioacchino Micheli, Giorgio Camilloni
Summary: This article proposes a hypothesis that the presence of introns in gene sequences may stabilize gene duplication, which is one of the driving forces in genome evolution. The article provides a review of the topic and a detailed explanation of the hypothesis.
Article
Biotechnology & Applied Microbiology
Nicolas S. M. Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer, Christian R. Voolstra, Oleg Simakov
Summary: This study analyzed 49 animal genomes and discovered the largest gains of synteny in the last common ancestor of bilaterians and cnidarians. Depending on their node of emergence, the novel syntenic blocks exhibit distinct functional compositions and gene density properties. These findings provide insights into the regulatory properties of microsyntenic blocks in animal genomes.
Article
Biotechnology & Applied Microbiology
Yulin Jin, Tao Zhou, Wansheng Jiang, Ning Li, Xiaoyan Xu, Suxu Tan, Huitong Shi, Yujia Yang, Zihao Yuan, Wenwen Wang, Guyu Qin, Shikai Liu, Dongya Gao, Rex Dunham, Zhanjiang Liu
Summary: This study identified genomic regions associated with resistance against enteric septicemia of catfish (ESC) and found different mechanisms of resistance in the liver and intestine. The study also highlighted the importance of apolipoproteins and downregulation of NCK in ESC resistance.
MARINE BIOTECHNOLOGY
(2022)
Article
Evolutionary Biology
Mark D. Scherz, Paul Masonick, Axel Meyer, C. Darrin Hulsey
Summary: Whole genome sequences provide important evidence for our understanding of phylogenetic relationships, but they may not be able to resolve the evolutionary history of rapidly radiating lineages. Integrating results from different methods and using phylogenomic approaches can help overcome these challenges.
SYSTEMATIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Andreas Harer, Yipeng Liang, Frederico Henning, Axel Meyer
Summary: This study uncovers the genetic basis of the gold/dark polymorphism in Midas cichlid fish by identifying a transposon insertion in the gene goldentouch.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Camila L. Nacif, Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Gonzalo Machado-Schiaffino, Axel Meyer, Frederico Henning
Summary: The evolution and differentiation of sex chromosomes is a significant event in genome evolution, and the repeated evolution and variability of sex-determination mechanisms in fishes make them a suitable model for studying general patterns in evolution. This study used forward-genetics, long-read sequencing, and optical mapping to determine that sex in Midas cichlids is determined by an XY system and identified and assembled the sex-determining region. The study also found that the male-specific region on chromosome 4 contains transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved as a master sex-determining gene. The duplication of anti-Mullerian genes is a common mechanism for establishing new sex determiners, highlighting the importance of molecular parallelism in the evolution of sex determination.
Article
Biology
Huihui Wang, Hong Yu, Qi Li, Shikai Liu
Summary: This study investigates the expression profiles of lncRNA in the gonads of Pacific oyster and predicts their potential functions in the regulatory mechanisms of gametogenesis. The results suggest that trans-regulatory lncRNAs play a vital role in the reproductive process. By constructing core networks of lncRNAs-mRNAs, several important lncRNAs are identified to regulate sterility-related genes. This research provides insights into the regulatory mechanism of lncRNAs in the gametogenesis of sterile triploid oysters.
Article
Fisheries
Yiming Hu, Qi Li, Chengxun Xu, Shikai Liu, Lingfeng Kong, Hong Yu
Summary: This study investigates the genetic diversity and structure of three generations of mass-selected lines and three wild populations of C. nippona. The results show that the genetic diversity of the selected lines is maintained, with minimal genetic differentiation among different lines. Significant genetic differentiation is observed among the wild populations, suggesting the presence of genetically isolated populations. To maximize future selective breeding efforts, the use of larger broodstock and a multi-line breeding strategy is recommended.
Article
Fisheries
Jianwen Gong, Qi Li, Hong Yu, Shikai Liu, Lingfeng Kong
Summary: This study investigated the physiological and immunological response of Crassostrea nippona to low salinity. The results showed that low salinity led to hyperosmolality in the hemolymph and differential gene expression in the gill transcriptome. The study provides insights into the immune mechanism of C. nippona under low salinity stress.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yulin Jin, Kenong Su, Ha Eun Kong, Wenjing Ma, Zhiqin Wang, Yujing Li, Ronghua Li, Emily G. Allen, Hao Wu, Peng Jin
Summary: DNA methylation plays a critical role in neuronal diversity and disease development in the brain. This study constructs DNA methylation maps for three cell types and uncovers cell type-specific DNA methylation signatures associated with functional characteristics of neuronal subtypes.
HUMAN MOLECULAR GENETICS
(2023)
Article
Genetics & Heredity
Wenbo Zhu, Zhongkai Wang, Haorong Li, Ping Li, Lili Ni, Li Jiao, Yandong Ren, Ping You
Summary: The study provides a high-quality genome assembly and annotation for the endangered freshwater fish Brachymystax tsinlingensis. The research reveals unique genomic features of salmonids, such as slow evolutionary rate, whole-genome duplication event, and muscle highly expressed genes related to migratory habits.
G3-GENES GENOMES GENETICS
(2022)
Article
Biology
Melissa B. DellaTorre, Francis T. C. Pan, Andrew W. Griffith, Ning Li, Donal T. Manahan
Summary: Understanding the physiological responses of Pacific oyster larvae to temperature variation is important for understanding their adaptation to environmental change. This study analyzed the variation in thermal sensitivity for respiration and protein synthesis among different larval families. The results showed that family played a significant role in determining the thermal sensitivity of these physiological processes, with some families exhibiting increased resilience to rising temperatures.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Engineering, Marine
Yiming Hu, Qi Li, Chengxun Xu, Shikai Liu, Lingfeng Kong, Hong Yu
Summary: This study investigated the differences in temperature and salinity tolerance between C. nippona and C. gigas spat and determined the optimal environmental conditions for the aquaculture of C. nippona spat. The results showed that C. nippona had lower survival rates than C. gigas under temperature changes and salinity decreases, but higher survival rates with increasing salinity. The findings suggest that particular attention should be paid to the inferior adaptability of C. nippona when farming outside their natural habitats.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Evolutionary Biology
Paul Masonick, Axel Meyer, Christopher Darrin Hulsey
Summary: The genomic loci underlying variation in vertebrate structures like lips are surprisingly predictable. Both adaptive and maladaptive variation in traits such as jaws and teeth can be structured by the same genes in evolutionarily disparate organisms like teleost fishes and mammals. The recurrence of hypertrophied lips in cichlid fish lineages suggests the presence of shared genetic bases and potential insights into the genetic factors influencing human craniofacial anomalies.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Ralf F. Schneider, Helen M. Gunter, Inken Salewski, Joost M. Woltering, Axel Meyer
Summary: Evolutionary novelties can promote ecological specialization and adaptive radiations. Belonoid fishes, such as flying fishes, halfbeaks, and needlefishes, have highly diversified elongated jaw phenotypes. In this study, the development of elongated jaws in a halfbeak and a needlefish was investigated, revealing that these jaws consist of distinct base and extension portions. The growth dynamics of both bases and extensions were described, and the molecular mechanisms underlying the extension outgrowth were deduced.
Review
Genetics & Heredity
Jacob L. Steenwyk, Yuanning Li, Xiaofan Zhou, Xing-Xing Shen, Antonis Rokas
Summary: The development of genome-scale data and new statistical phylogenetic approaches has greatly helped in reconstructing the tree of life, but incongruence still persists in phylogenomic data, which hampers our ability to interpret and reconstruct the tree. Incongruence can be caused by biological factors like incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination, and convergent molecular evolution, as well as analytical factors like stochastic, systematic, and treatment errors. This review discusses these factors, advances in methodology to identify and resolve incongruence, and future research directions.
NATURE REVIEWS GENETICS
(2023)